| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/SKCM-TM/5956385/SKCM-TM.rppa.txt |
| GDAC_TopgenesforCluster1 selectedgenes | ALL |
| GDAC_ConsensusClustering2 clustering algorithm | HIERARCHICAL |
| GDAC_ConsensusClustering2 cluster by | |
| GDAC_ConsensusClustering2 distance measure | PEARSON |
| GDAC_ConsensusClustering2 normalize type | |
| GDAC_selectBestcluster3 measure | Pearson |
| GDAC_selectBestcluster3 output | SKCM-TM |
| GDAC_selectBestcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/SKCM-TM/5956385/SKCM-TM.rppa.txt |
| GDAC_CnmfReports4 report | hclRppa |
| Execution Times: | |
| Submitted: | 19:46:33 26-01-14 |
| Completed: | |
| Elapsed: | 09 hrs 33 mins 46 secs |
step 1. GDAC_TopgenesforCluster [id: 502186] This module can be used to selecte top genes with most variation, convert file to gct format, as well as imput missing value
urn:lsid:broadinstitute.org:cancer.genome.analysis:00205:36
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/SKCM-TM/5956385/SKCM-TM.rppa.txt |
| selectedgenes | ALL |
| outputprefix | outputprefix |
| Output Files: | |
| .lsf.out | |
| outputprefix.expclu.gct | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:46:33 26-01-14 |
| Completed: | 19:56:29 26-01-14 |
| Elapsed: | 00 hrs 09 mins 55 secs |
step 2. GDAC_ConsensusClustering [id: 502187] Resampling-based clustering method
urn:lsid:broadinstitute.org:cancer.genome.analysis:00158:6
| input filename | outputprefix.expclu.gct |
| kmax | 8 |
| resampling iterations | 20 |
| seed value | 12345 |
| clustering algorithm | HIERARCHICAL |
| cluster by | |
| distance measure | PEARSON |
| resample | subsample |
| merge type | average |
| descent iterations | 2000 |
| output stub | <input.filename_basename> |
| normalize type | |
| normalization iterations | 0 |
| create heat map | -p |
| heat map size | 2 |
| Execution Times: | |
| Submitted: | 19:46:33 26-01-14 |
| Completed: | 05:19:34 27-01-14 |
| Elapsed: | 09 hrs 33 mins 00 secs |
step 3. GDAC_selectBestcluster [id: 502188]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:34
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| output | SKCM-TM |
| file clu 2 | outputprefix.expclu.sub136.2.clu |
| file clu 3 | outputprefix.expclu.sub136.3.clu |
| file clu 4 | outputprefix.expclu.sub136.4.clu |
| file clu 5 | outputprefix.expclu.sub136.5.clu |
| file clu 6 | outputprefix.expclu.sub136.6.clu |
| file clu 7 | outputprefix.expclu.sub136.7.clu |
| file clu 8 | outputprefix.expclu.sub136.8.clu |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/SKCM-TM/5956385/SKCM-TM.rppa.txt |
| Execution Times: | |
| Submitted: | 19:46:33 26-01-14 |
| Completed: | 05:20:01 27-01-14 |
| Elapsed: | 09 hrs 33 mins 28 secs |
step 4. GDAC_CnmfReports [id: 502189]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:32
| kclus | SKCM-TM.silfig.png |
| markers | SKCM-TM.subclassmarkers.txt |
| bestclu | SKCM-TM.bestclus.txt |
| allcluster | SKCM-TM.allclusters.txt |
| cormatrix | SKCM-TM.cormatrix.png |
| file gif 2 | outputprefix.expclu.sub136.srt.2.gif |
| file gif 3 | outputprefix.expclu.sub136.srt.3.gif |
| file gif 4 | outputprefix.expclu.sub136.srt.4.gif |
| file gif 5 | outputprefix.expclu.sub136.srt.5.gif |
| file gif 6 | outputprefix.expclu.sub136.srt.6.gif |
| file gif 7 | outputprefix.expclu.sub136.srt.7.gif |
| file gif 8 | outputprefix.expclu.sub136.srt.8.gif |
| expdata | outputprefix.expclu.gct |
| markersP | SKCM-TM.seclectedSubclassmarkers.txt |
| heatmap | SKCM-TM.geneheatmap.png |
| heatmapall | SKCM-TM.geneheatmaptopgenes.png |
| report | hclRppa |
| Output Files: | |
| nozzle.html | |
| .lsf.out | |
| nozzle.RData | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:46:33 26-01-14 |
| Completed: | 05:20:19 27-01-14 |
| Elapsed: | 09 hrs 33 mins 45 secs |
